1. check if the bootmode configuration is correct or not
2. make sure eMMC is power before any other power
3. try and add a serial resistor on the eMMC clock signal, and a capacitor to ground, and adjust the resistor and capacitor value to see if it helps.
for resistor, try 10ohm ~ 100ohm, capacitor, try 10pF~47pF.
We found something strange with the eMMC clock, need to add some resistor and capacitor to delay or deform the signal before eMMC can bootup correctly some time.